Multiple sequence alignment - TraesCS5A01G083700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G083700 chr5A 100.000 2816 0 0 1 2816 109345572 109342757 0.000000e+00 5201.0
1 TraesCS5A01G083700 chr5A 91.977 511 31 3 3 513 368150882 368151382 0.000000e+00 708.0
2 TraesCS5A01G083700 chr5D 93.534 1160 60 7 651 1807 105350788 105349641 0.000000e+00 1712.0
3 TraesCS5A01G083700 chr5D 96.318 679 24 1 2138 2816 105349287 105348610 0.000000e+00 1114.0
4 TraesCS5A01G083700 chr5D 89.691 291 21 5 1839 2121 105349561 105349272 2.060000e-96 363.0
5 TraesCS5A01G083700 chr5D 97.368 38 1 0 1800 1837 105349635 105349598 6.510000e-07 65.8
6 TraesCS5A01G083700 chr5B 94.004 984 31 11 1839 2816 115319013 115318052 0.000000e+00 1465.0
7 TraesCS5A01G083700 chr5B 90.278 864 54 14 649 1492 115320298 115319445 0.000000e+00 1103.0
8 TraesCS5A01G083700 chr5B 91.409 582 36 6 1270 1837 115319631 115319050 0.000000e+00 785.0
9 TraesCS5A01G083700 chr5B 84.021 194 24 3 1234 1420 115319620 115319427 2.230000e-41 180.0
10 TraesCS5A01G083700 chr7A 91.346 624 37 10 3 614 325896877 325896259 0.000000e+00 837.0
11 TraesCS5A01G083700 chr2A 91.228 570 38 7 3 570 716407235 716406676 0.000000e+00 765.0
12 TraesCS5A01G083700 chr2A 91.281 562 39 4 1 553 726863327 726863887 0.000000e+00 758.0
13 TraesCS5A01G083700 chr2A 88.073 545 55 6 10 554 163683343 163682809 3.060000e-179 638.0
14 TraesCS5A01G083700 chr2A 94.444 144 8 0 1 144 209062052 209062195 3.650000e-54 222.0
15 TraesCS5A01G083700 chr2A 94.776 134 7 0 1 134 616641618 616641485 2.840000e-50 209.0
16 TraesCS5A01G083700 chr2A 95.798 119 5 0 1 119 449233296 449233178 2.860000e-45 193.0
17 TraesCS5A01G083700 chr1A 89.855 552 45 8 71 614 491499051 491498503 0.000000e+00 699.0
18 TraesCS5A01G083700 chr4A 93.763 465 22 4 156 614 462074848 462074385 0.000000e+00 691.0
19 TraesCS5A01G083700 chr3A 87.458 598 63 9 1 593 549929298 549928708 0.000000e+00 678.0
20 TraesCS5A01G083700 chrUn 87.978 549 54 9 74 613 290876063 290876608 3.060000e-179 638.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G083700 chr5A 109342757 109345572 2815 True 5201.00 5201 100.00000 1 2816 1 chr5A.!!$R1 2815
1 TraesCS5A01G083700 chr5A 368150882 368151382 500 False 708.00 708 91.97700 3 513 1 chr5A.!!$F1 510
2 TraesCS5A01G083700 chr5D 105348610 105350788 2178 True 813.70 1712 94.22775 651 2816 4 chr5D.!!$R1 2165
3 TraesCS5A01G083700 chr5B 115318052 115320298 2246 True 883.25 1465 89.92800 649 2816 4 chr5B.!!$R1 2167
4 TraesCS5A01G083700 chr7A 325896259 325896877 618 True 837.00 837 91.34600 3 614 1 chr7A.!!$R1 611
5 TraesCS5A01G083700 chr2A 716406676 716407235 559 True 765.00 765 91.22800 3 570 1 chr2A.!!$R4 567
6 TraesCS5A01G083700 chr2A 726863327 726863887 560 False 758.00 758 91.28100 1 553 1 chr2A.!!$F2 552
7 TraesCS5A01G083700 chr2A 163682809 163683343 534 True 638.00 638 88.07300 10 554 1 chr2A.!!$R1 544
8 TraesCS5A01G083700 chr1A 491498503 491499051 548 True 699.00 699 89.85500 71 614 1 chr1A.!!$R1 543
9 TraesCS5A01G083700 chr3A 549928708 549929298 590 True 678.00 678 87.45800 1 593 1 chr3A.!!$R1 592
10 TraesCS5A01G083700 chrUn 290876063 290876608 545 False 638.00 638 87.97800 74 613 1 chrUn.!!$F1 539


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
641 682 0.033109 AGGGGGTAGCATTTTGGCTC 60.033 55.0 0.0 0.0 44.54 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 2762 0.255033 AGCCATCAAGCATCAGAGCA 59.745 50.0 0.0 0.0 36.85 4.26 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.531280 CCATAGCTTTCCAACGATATATCAG 57.469 40.000 13.11 8.01 0.00 2.90
51 55 4.340617 CCCATTTGGACACCTTTTAGCTA 58.659 43.478 0.00 0.00 37.39 3.32
505 541 7.575414 TTACGGTGCATTGATGGTAAAATAT 57.425 32.000 0.00 0.00 0.00 1.28
513 549 6.378280 GCATTGATGGTAAAATATAGGAGGGG 59.622 42.308 0.00 0.00 0.00 4.79
535 571 6.455690 GGGGGAGAATAACTATTCCTCATT 57.544 41.667 5.95 0.00 42.29 2.57
537 573 6.166982 GGGGAGAATAACTATTCCTCATTCG 58.833 44.000 5.95 0.00 42.29 3.34
631 672 1.742308 TAATGGATGGAGGGGGTAGC 58.258 55.000 0.00 0.00 0.00 3.58
632 673 0.328450 AATGGATGGAGGGGGTAGCA 60.328 55.000 0.00 0.00 0.00 3.49
633 674 0.103715 ATGGATGGAGGGGGTAGCAT 60.104 55.000 0.00 0.00 0.00 3.79
634 675 0.328450 TGGATGGAGGGGGTAGCATT 60.328 55.000 0.00 0.00 0.00 3.56
635 676 0.853530 GGATGGAGGGGGTAGCATTT 59.146 55.000 0.00 0.00 0.00 2.32
636 677 1.217942 GGATGGAGGGGGTAGCATTTT 59.782 52.381 0.00 0.00 0.00 1.82
637 678 2.310538 GATGGAGGGGGTAGCATTTTG 58.689 52.381 0.00 0.00 0.00 2.44
638 679 0.334676 TGGAGGGGGTAGCATTTTGG 59.665 55.000 0.00 0.00 0.00 3.28
639 680 1.043116 GGAGGGGGTAGCATTTTGGC 61.043 60.000 0.00 0.00 0.00 4.52
641 682 0.033109 AGGGGGTAGCATTTTGGCTC 60.033 55.000 0.00 0.00 44.54 4.70
642 683 1.384222 GGGGGTAGCATTTTGGCTCG 61.384 60.000 0.00 0.00 44.54 5.03
643 684 1.384222 GGGGTAGCATTTTGGCTCGG 61.384 60.000 0.00 0.00 44.54 4.63
644 685 0.679960 GGGTAGCATTTTGGCTCGGT 60.680 55.000 0.00 0.00 44.54 4.69
645 686 1.173913 GGTAGCATTTTGGCTCGGTT 58.826 50.000 0.00 0.00 44.54 4.44
646 687 1.544246 GGTAGCATTTTGGCTCGGTTT 59.456 47.619 0.00 0.00 44.54 3.27
647 688 2.750712 GGTAGCATTTTGGCTCGGTTTA 59.249 45.455 0.00 0.00 44.54 2.01
655 696 4.811969 TTTGGCTCGGTTTATGTCTCTA 57.188 40.909 0.00 0.00 0.00 2.43
656 697 4.811969 TTGGCTCGGTTTATGTCTCTAA 57.188 40.909 0.00 0.00 0.00 2.10
685 726 1.467734 GAGTAGTCGAGAAGGAACGCA 59.532 52.381 0.00 0.00 0.00 5.24
705 746 4.349501 GCATAGCAAAAGCAGAGACAATC 58.650 43.478 0.00 0.00 0.00 2.67
776 819 1.068417 CCACTTGTTCGTGTCCGGA 59.932 57.895 0.00 0.00 33.07 5.14
1017 1063 5.021458 CCGGGCCTATAAATCCTCTACTAA 58.979 45.833 0.84 0.00 0.00 2.24
1018 1064 5.661759 CCGGGCCTATAAATCCTCTACTAAT 59.338 44.000 0.84 0.00 0.00 1.73
1021 1067 7.566569 GGGCCTATAAATCCTCTACTAATTCC 58.433 42.308 0.84 0.00 0.00 3.01
1144 1194 1.496393 CTTCTCGCTGTGCTTGCTG 59.504 57.895 0.00 0.00 0.00 4.41
1362 1478 0.032912 AAACCAGACCCAAAACCGGT 60.033 50.000 0.00 0.00 35.88 5.28
1379 1495 1.966451 GTGCCGAAACCTGACCCAG 60.966 63.158 0.00 0.00 0.00 4.45
1429 1545 1.943730 AACCTGACCCAGCACCCAAA 61.944 55.000 0.00 0.00 0.00 3.28
1550 1666 3.253838 CGGACCCCAAACCCCAGA 61.254 66.667 0.00 0.00 0.00 3.86
1561 1677 4.323477 CCCCAGACGCCGGAACAA 62.323 66.667 5.05 0.00 0.00 2.83
1693 1809 1.067635 GCATGGGTGTTGGTGCTTAAG 60.068 52.381 0.00 0.00 34.85 1.85
1705 1821 2.028748 GGTGCTTAAGTTGTCTCCGGTA 60.029 50.000 0.00 0.00 0.00 4.02
1782 1900 2.254546 TGTTCGTGTGAGCCATCTTT 57.745 45.000 0.00 0.00 0.00 2.52
1793 1911 0.110056 GCCATCTTTGCGTCAGTGTG 60.110 55.000 0.00 0.00 0.00 3.82
1833 1964 6.248433 ACCATGAATAAACAGAGGAACATGT 58.752 36.000 0.00 0.00 34.17 3.21
1837 1968 8.562892 CATGAATAAACAGAGGAACATGTATCC 58.437 37.037 15.33 15.33 37.22 2.59
1853 2019 4.599041 TGTATCCCACTTGATTTTCTGGG 58.401 43.478 0.00 0.00 44.41 4.45
1899 2065 9.535878 CTAGTACCACTCCTTTAATTTCATCTC 57.464 37.037 0.00 0.00 0.00 2.75
1910 2076 7.201496 CCTTTAATTTCATCTCTGTTGCAATGC 60.201 37.037 0.59 0.00 0.00 3.56
1939 2105 4.094294 TGTTCCTTCAACTATGCGTATTGC 59.906 41.667 0.00 0.00 38.98 3.56
1961 2127 8.719560 TTGCGTAGTGTTCCATAATATTTGTA 57.280 30.769 0.00 0.00 0.00 2.41
1998 2171 1.109323 AGGCAGGGCACTTGACAAAC 61.109 55.000 0.00 0.00 0.00 2.93
2034 2208 7.591426 CAGAACTTAATTCCTCAAACGAAAAGG 59.409 37.037 0.00 0.00 38.16 3.11
2051 2226 6.151480 ACGAAAAGGAAAAACAGAACTTACCA 59.849 34.615 0.00 0.00 0.00 3.25
2082 2259 1.616159 TAGAACTTGGGCCTGTTTGC 58.384 50.000 14.62 5.60 0.00 3.68
2113 2290 6.030849 CGATATCGGGTCAGTCAGATTATTC 58.969 44.000 17.51 0.00 35.37 1.75
2161 2340 3.956199 ACTATTTTGCAGGTGGATCATGG 59.044 43.478 0.00 0.00 0.00 3.66
2175 2354 3.245371 GGATCATGGCCCATATGGAAAGA 60.245 47.826 24.00 12.97 37.39 2.52
2290 2469 2.542595 GTGGTTCCTGTAACAAGACACG 59.457 50.000 0.00 0.00 40.08 4.49
2296 2475 2.736721 CCTGTAACAAGACACGGTCATG 59.263 50.000 6.78 7.13 37.30 3.07
2309 2488 1.402787 GGTCATGGGCAATAACAGGG 58.597 55.000 0.00 0.00 0.00 4.45
2331 2510 2.861462 TTGAAAAGTGGCAGGAAACG 57.139 45.000 0.00 0.00 0.00 3.60
2583 2762 3.885297 CACCGAAATAGGATTTGCCTCAT 59.115 43.478 0.00 0.00 46.97 2.90
2655 2834 2.419297 GCCAAAGGAGATGACGAGTGAT 60.419 50.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.074929 TGTCCAAATGGGGCTTCTGATATAT 59.925 40.000 0.00 0.00 43.75 0.86
24 25 0.251787 AGGTGTCCAAATGGGGCTTC 60.252 55.000 0.00 0.00 43.75 3.86
51 55 3.260128 CCCCGAGTACTAGGTTGAACTTT 59.740 47.826 19.33 0.00 0.00 2.66
126 132 5.359194 AACACTATTCTGATCACGGGATT 57.641 39.130 0.00 0.00 32.67 3.01
249 280 7.970384 TGTAACTATTTGAATTCCAAGCGTAG 58.030 34.615 2.27 0.55 35.94 3.51
325 360 9.768662 AAACTGCAAATTTTCTTGTCTTATGAT 57.231 25.926 0.00 0.00 0.00 2.45
513 549 6.166982 CGAATGAGGAATAGTTATTCTCCCC 58.833 44.000 10.71 0.00 41.33 4.81
515 551 6.994221 TCCGAATGAGGAATAGTTATTCTCC 58.006 40.000 10.71 5.10 41.33 3.71
535 571 4.696899 ATATCGCTATTCGTCATTCCGA 57.303 40.909 0.00 0.00 39.67 4.55
614 655 0.103715 ATGCTACCCCCTCCATCCAT 60.104 55.000 0.00 0.00 0.00 3.41
615 656 0.328450 AATGCTACCCCCTCCATCCA 60.328 55.000 0.00 0.00 0.00 3.41
616 657 0.853530 AAATGCTACCCCCTCCATCC 59.146 55.000 0.00 0.00 0.00 3.51
617 658 2.310538 CAAAATGCTACCCCCTCCATC 58.689 52.381 0.00 0.00 0.00 3.51
618 659 1.062962 CCAAAATGCTACCCCCTCCAT 60.063 52.381 0.00 0.00 0.00 3.41
619 660 0.334676 CCAAAATGCTACCCCCTCCA 59.665 55.000 0.00 0.00 0.00 3.86
620 661 1.043116 GCCAAAATGCTACCCCCTCC 61.043 60.000 0.00 0.00 0.00 4.30
621 662 0.033109 AGCCAAAATGCTACCCCCTC 60.033 55.000 0.00 0.00 40.56 4.30
622 663 0.033109 GAGCCAAAATGCTACCCCCT 60.033 55.000 0.00 0.00 42.95 4.79
623 664 1.384222 CGAGCCAAAATGCTACCCCC 61.384 60.000 0.00 0.00 42.95 5.40
624 665 1.384222 CCGAGCCAAAATGCTACCCC 61.384 60.000 0.00 0.00 42.95 4.95
625 666 0.679960 ACCGAGCCAAAATGCTACCC 60.680 55.000 0.00 0.00 42.95 3.69
626 667 1.173913 AACCGAGCCAAAATGCTACC 58.826 50.000 0.00 0.00 42.95 3.18
627 668 4.142469 ACATAAACCGAGCCAAAATGCTAC 60.142 41.667 0.00 0.00 42.95 3.58
628 669 4.013728 ACATAAACCGAGCCAAAATGCTA 58.986 39.130 0.00 0.00 42.95 3.49
629 670 2.825532 ACATAAACCGAGCCAAAATGCT 59.174 40.909 0.00 0.00 46.37 3.79
630 671 3.119495 AGACATAAACCGAGCCAAAATGC 60.119 43.478 0.00 0.00 0.00 3.56
631 672 4.396166 AGAGACATAAACCGAGCCAAAATG 59.604 41.667 0.00 0.00 0.00 2.32
632 673 4.589908 AGAGACATAAACCGAGCCAAAAT 58.410 39.130 0.00 0.00 0.00 1.82
633 674 4.015872 AGAGACATAAACCGAGCCAAAA 57.984 40.909 0.00 0.00 0.00 2.44
634 675 3.695830 AGAGACATAAACCGAGCCAAA 57.304 42.857 0.00 0.00 0.00 3.28
635 676 4.464951 TCTTAGAGACATAAACCGAGCCAA 59.535 41.667 0.00 0.00 0.00 4.52
636 677 4.021229 TCTTAGAGACATAAACCGAGCCA 58.979 43.478 0.00 0.00 0.00 4.75
637 678 4.650754 TCTTAGAGACATAAACCGAGCC 57.349 45.455 0.00 0.00 0.00 4.70
638 679 4.985409 CCATCTTAGAGACATAAACCGAGC 59.015 45.833 0.00 0.00 0.00 5.03
639 680 6.392625 TCCATCTTAGAGACATAAACCGAG 57.607 41.667 0.00 0.00 0.00 4.63
640 681 6.294010 CGATCCATCTTAGAGACATAAACCGA 60.294 42.308 0.00 0.00 0.00 4.69
641 682 5.859114 CGATCCATCTTAGAGACATAAACCG 59.141 44.000 0.00 0.00 0.00 4.44
642 683 6.982852 TCGATCCATCTTAGAGACATAAACC 58.017 40.000 0.00 0.00 0.00 3.27
643 684 7.653647 ACTCGATCCATCTTAGAGACATAAAC 58.346 38.462 0.00 0.00 33.53 2.01
644 685 7.825331 ACTCGATCCATCTTAGAGACATAAA 57.175 36.000 0.00 0.00 33.53 1.40
645 686 8.158132 ACTACTCGATCCATCTTAGAGACATAA 58.842 37.037 0.00 0.00 33.53 1.90
646 687 7.681679 ACTACTCGATCCATCTTAGAGACATA 58.318 38.462 0.00 0.00 33.53 2.29
647 688 6.539173 ACTACTCGATCCATCTTAGAGACAT 58.461 40.000 0.00 0.00 33.53 3.06
705 746 1.983972 CTCCACCTTCGTCTTCTTCG 58.016 55.000 0.00 0.00 0.00 3.79
776 819 1.528776 GCGAGATCTAGGACCCCGT 60.529 63.158 4.92 0.00 0.00 5.28
1017 1063 0.884704 GTGTGAGTGTGTGGCGGAAT 60.885 55.000 0.00 0.00 0.00 3.01
1018 1064 1.522806 GTGTGAGTGTGTGGCGGAA 60.523 57.895 0.00 0.00 0.00 4.30
1021 1067 2.885676 GCTGTGTGAGTGTGTGGCG 61.886 63.158 0.00 0.00 0.00 5.69
1050 1096 4.452455 GCTCACTTGCTTTGTAGTATGTGT 59.548 41.667 0.00 0.00 40.57 3.72
1121 1171 4.742201 GCACAGCGAGAAGGCGGA 62.742 66.667 0.00 0.00 38.18 5.54
1362 1478 2.429930 CTGGGTCAGGTTTCGGCA 59.570 61.111 0.00 0.00 0.00 5.69
1396 1512 4.693525 GGTTTCGGCGCCGGTTTG 62.694 66.667 44.95 20.64 40.25 2.93
1429 1545 2.448931 TCTGGTTTGGGGTCGGGT 60.449 61.111 0.00 0.00 0.00 5.28
1470 1586 4.659172 TGGGGTCAGGCTTTGGCG 62.659 66.667 0.00 0.00 39.81 5.69
1550 1666 2.433664 GGACGATTGTTCCGGCGT 60.434 61.111 6.01 0.00 39.99 5.68
1561 1677 3.417275 CTTCGGCTGCGAGGACGAT 62.417 63.158 6.82 0.00 46.55 3.73
1693 1809 4.198028 ACTAACCATTACCGGAGACAAC 57.802 45.455 9.46 0.00 0.00 3.32
1705 1821 8.292444 ACACATGCAATACATTACTAACCATT 57.708 30.769 0.00 0.00 36.64 3.16
1782 1900 2.734591 GGGAGACACACTGACGCA 59.265 61.111 0.00 0.00 0.00 5.24
1793 1911 0.892755 TGGTACATCACACGGGAGAC 59.107 55.000 0.00 0.00 0.00 3.36
1837 1968 3.799917 GCAACACCCAGAAAATCAAGTGG 60.800 47.826 0.00 0.00 0.00 4.00
1853 2019 3.936564 AGAGAAGGAATGAGAGCAACAC 58.063 45.455 0.00 0.00 0.00 3.32
1899 2065 3.922240 GGAACACAATAGCATTGCAACAG 59.078 43.478 11.91 0.00 0.00 3.16
1910 2076 5.351465 ACGCATAGTTGAAGGAACACAATAG 59.649 40.000 0.00 0.00 36.98 1.73
1961 2127 2.621668 GCCTTTCCATTTCCCAGTAGCT 60.622 50.000 0.00 0.00 0.00 3.32
2034 2208 7.810759 TGAAACTGTTGGTAAGTTCTGTTTTTC 59.189 33.333 0.00 0.00 36.87 2.29
2051 2226 4.338400 GCCCAAGTTCTAACTGAAACTGTT 59.662 41.667 0.00 0.00 39.66 3.16
2134 2311 3.686016 TCCACCTGCAAAATAGTCTTCC 58.314 45.455 0.00 0.00 0.00 3.46
2135 2312 4.943705 TGATCCACCTGCAAAATAGTCTTC 59.056 41.667 0.00 0.00 0.00 2.87
2140 2319 3.243636 GCCATGATCCACCTGCAAAATAG 60.244 47.826 0.00 0.00 0.00 1.73
2161 2340 3.845781 TCTCTGTCTTTCCATATGGGC 57.154 47.619 21.78 7.84 36.21 5.36
2272 2451 2.798847 GACCGTGTCTTGTTACAGGAAC 59.201 50.000 0.00 0.11 37.42 3.62
2290 2469 1.402787 CCCTGTTATTGCCCATGACC 58.597 55.000 0.00 0.00 0.00 4.02
2296 2475 2.452600 TCAATCCCCTGTTATTGCCC 57.547 50.000 0.00 0.00 33.91 5.36
2309 2488 3.653344 GTTTCCTGCCACTTTTCAATCC 58.347 45.455 0.00 0.00 0.00 3.01
2331 2510 0.729690 GAGAGTCGGCCTTGCATTTC 59.270 55.000 0.00 0.00 0.00 2.17
2583 2762 0.255033 AGCCATCAAGCATCAGAGCA 59.745 50.000 0.00 0.00 36.85 4.26
2655 2834 2.804986 TGCTTATCTTGATGGCCACA 57.195 45.000 8.16 5.62 0.00 4.17



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.